At the end of the Second Age, there were Silvan Elves living in the western vales of these hills, though at that time the hills were known as Emyn Duir, the Dark Mountains. That name referred only to the dense shade of the trees, and not to the Shadow that would pass through the Forest and eventually lead to its becoming known as 'Mirkwood'. That same Shadow of Sauron caused the Elves of these hills to remove to the northern fringes of the Forest, where they established the Woodland Realm.

The encroaching darkness was also the cause of the change of name from Emyn Duir to Emyn-nu-Fuin 'hills under nightshade'. We do not have sufficiently detailed dating evidence to say whether there were still Elves in these hills at the time they became known as Emyn-nu-Fuin, but given that they were fleeing the Shadow that gave rise to that name, on balance it seems likely that they would already have departed.

When the darkness of Sauron began to spread through the Greenwood of Eryn Galen, it gained a new Elvish name borrowed from the First Age. That name was Taur-nu-Fuin, literally 'Forest under Nightshade' but usually translated 'Mirkwood'. At that time the hills within the Forest gained a new name of their own, Emyn-nu-Fuin, that mirrored that of the Forest as a whole. The name Taur-nu-Fuin had originated from another forest of the First Age that had similarly come under the power of the Dark Lord, the wooded northern highland that had formerly been known as Dorthonion.

The creatures that began to infest the mountains are not described in any detail, but we might surmise that these were - at least in part - the giant spiders also found elsewhere in northern Mirkwood. It is telling that a stream that ran northward out of Emyn-nu-Fuin, the Enchanted River, had black water, and drinking this water would cause a deep enchanted sleep. Similar dark streams were described in the valley of Ered Gorgoroth during the First Age, whose mountains were also infested with unnatural spiders of the same kind.